Beyond Darkness
by CommanderJames
Summary: After a 4 year romance with the doctor, Susan develops the feelings she knew she would for James T. Kirk. During her confusion, an old fling comes along threatening to destroy everything...John Harrison. Will Susan make the sacrifices she needs too, or realize she needs to tell Kirk how she feels...but shes too late? The third installment to the Susan Jones trilogy!
1. Chapter 1

**A/N: Okay guys here's the Third installment of my Susan Jones Trilogy! This takes place during STID so there are spoilers! You can read this one without the other 2, but there are some references you may miss so i suggest reading the first one 'Forever United' and the second one 'Changing Back Time'. I update as i get Favorites/Follows/Reviews!**

**I own Nothing except Captain Susan Jones, Commander Cassie Moore, and The U.S.S Centerville and her crew.**

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Ch. 1

*4 years and hundreds of successful missions later.*

Bones was off planet. I hated it. I knew it was our job, but I missed his warmth when he would hold me at night, or the sound of his laugh when I told a not-so-funny joke, 4 years I've been with him, and not once did I bring up the conversation I heard between him and Jim. Even after he told me he loved me, or when we celebrated our first anniversary on the bay where he first asked me out and where we had our first official date. I didn't want to know the truth. Was I destined to die? I put the question back where it belonged, in my chest of unanswered questions.

"Captain, are you coming?" said Cassie. She cut her blonde hair right before her shoulders, the scar above her eye was a bit faded, but was now apart of her.

"Yes Commander, I'll ride the captains shuttle. See you there." I said turning and walking to the smaller shuttle across the deck.

"Admiral James to Captain Jones" said the voice over my com. I removed it from my boot and opened it. "Jones here." I spoke.

"Are you ready for your mission?" he asked enthusiastically.

"Aye sir." I said. They told me it was a top secret mission. Therefore he had to tell it to me in private.

"Your mission is to-" the com cut to static when the shuttle took off.

"that's odd" I said quietly to myself. I was the only one on the shuttle so I couldn't ask anyone else to use theirs. I stuck the com back in my boot. I looked out the window. Something caught my attention, we were flying away from the Centerville. I stood up and grabbed a phaser from under my seat and made my way to the cockpit. I reached my hand out to the door handle.

"I wouldn't do that if I we're you." I heard a voice behind me. A voice that sent cold shivers down my spine. I stopped. I didn't turn around.

"Who are you?" I said my phaser still pointed in front of me.

"Why Susan, it breaks my heart that you don't remember me. Admiral Marcus did a fine job keeping you quiet." he said the English accent giving him away.

"John." I said turning to his face. His piercing eyes caught me first. They were menacing. Hateful. I threw down my phaser."What are you doing?" I said. He removed his hood from his head. His hair was a little longer than I remember.

"you know exactly why I'm here. My crew." he said through clenched teeth.

"You know I had nothing to do with where your crew was sent." I said softly. I tried not to test him, i knew what he was capable of.

"Where are they?" he asked not believing my first statement.

"Marcus did something with them, he kept me in the dark." I said truthfully. He knew at that point I wasn't lying. He eyed me a bit before turning his back.

"What are you doing with me?" I said before he left. He turned to look at me. A smile crept up on his face.

"Well. I need a reason for them to come after me, and I believe you will do the trick." he said, his voice was so...cold.

"You seriously think that Admiral Marcus will send out a fleet of starships to recover the one person who knows all of his dirty little secrets?" I said sitting down in a chair that was facing him.

"You're right." he said placing his hood back onto his head. "But there are a few tricks up my sleeve to recover those missiles Susan. You are only part of it. When I kill Captain Pike, and kidnap you, who do you think is going to come after me?" he said leaning against a chair. I sat there in disbelief.

"you're gonna have Kirk and Bones come after you with the missiles." I said the pieces clicking into place. "John leave them alone!" I said standing up from my chair. He turned to look at me.

"Its only fair. You took those i loved away from me, now i will take the 2 men you love away from you." he said. He turned his back once more but didn't move. He looked over his shoulder, all I saw was the outline of his nose. "You once loved me Susan. What happened?" he said. A small ounce of hurt spread into his voice. I let a small laugh escape me.

"You know what happened. You used me Harrison. My intellect. My youth. My immaturity. I was only 19 when I loved you, and it was an honest mistake" I said. I shook my head and turned my back to him while returning to my seat. I looked out the window, there was nothing around us but space.

"I did love you. I hope you know that." he paused taking a deep breath. "Goodbye Susan." he said. A small compartment door opened in the back, and he was gone.

...

McCoys P.O.V

"Admiral James to Dr. McCoy." I heard from my com sitting on my desk in my office. I never got the chance to catch Susan before she left.

"McCoy here." I said. Standing up to stretch.

"McCoy we need you to our office with Captain Kirk and Commander Spock. Its urgent." he said the tone in his voice worried me.

"Aye sir. I'll be there with them both." I said grabbing a few utensils off my desk. "Thanks McCoy. James out." he said. I closed my com and re-opened it again. "McCoy to Spock." I spoke into the small device.

"Yes Doctor." Spocks voice came over the intercom.

"Admiral James' office. Its urgent. I'll meet you there. Get Jim." I said walking out of my office in my white doctors uniform.

"Yes Doctor." he said. The com went dead. I closed it and slipped the small device into the pocket of my all white uniform. I wound through hallways of the Starfleet HQ. Cadets running to and from class. I finally reached Admiral James' office, when Spock and Jim ran up.

"You know what this is about?" asked Jim. He was a tad out of breath.

"No idea." I said knocking on the door. I opened the opened it and walked in without waiting for a response, I was too impatient.

"Ahh. Yes, please have a seat guys." said the admiral. "I'm afraid we have some terrible news." he said his eyes tried their hardest to avoid mine. "It seems as if Captain Jones has gone missing. We suspect a kidnapping by one John Harrison. We are not sure where she has gone, but we have to suspect the worst." he said. I stared at the admiral. I couldn't move. Every inch of my body was In shock. I heard my name being called, but it was like I was underwater. The voices were mumbles, my vision was blurry. I looked up. Jim was standing in front of me his hands on my shoulder.

"we're going to find her." he said. Even though he wasn't with Su, I knew he still had feelings for her. He loved her. I stayed quiet and nodded my head. The admiral Continued to speak, but I stood up out of my chair and left back to my room. Su was gone. Su was gone. Su was gone. Su was gone...and that's all that filled my head.


	2. Chapter 2

**A/N: Alright I got 2 follows and a favorite so I may post more today depending on if I have the not, if I don't, then do expect a Ch. Tomorrow. I post as I get favorites/follows/reviews! **

**I own nothing except Captain Susan Jones, Commander Cassie Moore, and the U.S.S Centerville and her crew**

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Ch. 2

We landed on a planet pretty far from earth. I looked around. "Kronos" I whispered to myself. I picked my phaser up and pointed it at the cockpit and waited. No one walked out. I walked up to it and pressed the small button on the side. The doors slid open and I walked in. No one was driving the shuttle the whole time. it was on autopilot and I was alone. I quickly ran to the pilot seat and typed in the manual override code.

"Access failed. System shut down." said the computer.

"No no no!" I yelled slamming my hand on the screen. I pulled my com out of my boot. I opened it. The line was clear. "Yes!" I said thinking of who to call. "Jones to McCoy!" I said franticly

"McCoy here" the voice came over the intercom. He sounded depressed, upset. They must have told him.

"Bones its Su! I've been kidnapped by John Harrison! I've been taken to a remote location on Kronos! Do you copy?" I yelled crossing my fingers.

"Su I got your location! Stay there!" he said I heard footsteps. "Sulu! Its Su! She's on Kronos! Harrison took her!" I heard him explain. "We have to let Kirk know!" he said I heard someone in the background stating Starfleet Code I would have guesses Spock, but the voice didn't quite match up. "Su we're comin' to get chya! What's the shuttle code!" he yelled..

"Tracking the shuttle isn't going to work, the shuttle shut down. But if you can track my life force, you may be able to find me." just then a door at the back of the shuttle opened. I shut my com and crouched in a corner.

"Susan. I know you're in here."said John. His footsteps were loud and heavy. He walked a few feet before a voice came over a com he had in his pocket.

"Attention John Harrison, This is Captain Hikaru Sulu of the U.S.S. Enterprise, we currently are locked on to your location with highly advanced long range missiles, a group of highly trained officers are on their way to your location. You will surrender to them and hand over your prisoner Captain Susan Jones. You have 2 minutes to confirm your corporation. If you do not, it will lead to your obliteration." John closed his com with a little chuckle. He continued to walk towards me.

"Susan, lets go dear, my crew is waiting." he said. I heard him press the button for the cockpit. I raised my phaser. "Dear, you know that won't do you much good." he said yanking the phaser from my hands. He picked me up and threw me over his shoulder.

"John! Put me down!" I yelled wiggling the best I could. He was too strong.

"Susan please stop moving around. You're embarrassing yourself." he said.

"where are we going?" I said as I decided to just fall limp over his shoulder. There was no use in fighting. I might as well save my energy.

"to help your other boyfriend. If I am right. He should be getting ready to fight Klingons right about now." he said grabbing several weapons from a chest that was laying on the ground close to the shuttle.

"Damnit John!" I yelled. I was helpless. We continued walking for several minutes.

"Ahh we're almost there" he said setting me down on the ground. "Be quiet, and don't move" he said jumping onto the platform in front of us I looked around for anything I could use as a weapon. John started firing and a Klingon fell dead not to far away. I stood up and ran over to it. Its weapon laid idle beside It.

"Huh...how about that." I said to myself. I grabbed it and made me my way over to the center of the mess. "Jim!" I yelled. He was laying on the ground, a Klingon holding him. I lifted the gun and fired, the Klingon fell down next to him. A few seconds later, a Klingon was running my way. The weapon I used was out of ammunition. I threw it down and grabbed a knife that was laying close to another dead Klingon. I turned my attention back to the approaching Klingon. He ran at me with a vengeance. I brought my fist to his face. My knuckles split, but I barely felt it. He staggered back a few feet before running at me again. I positioned the blades in my hand and jabbed I upright into the torso. He fell to the ground. I picked up a smaller phaser in a half dead Klingons belt. I looked over to Harrison, he was now on the ground throwing knifes at them like he was a superhero. I looked over and saw Spock and Uhura. Both raced to Jims side. I ran after them, but Harrison caught me by the waist. I raised my weapon at him, but he removed it from my hand with ease and pointed it to my head.

"How many are there?" he said looking to the three. I struggled the best I could, but gave up. John looked to me and smiled before looking back to the group. "How many missiles?!" he yelled. Spock looked to Jim. He nodded his head.

"72" said Spock looking up to the man. John looked to me, then to Jim.

"I surrender" he said letting me go and throwing the weapon down. Spock grabbed it off the ground and pointed it at him. I stood up and ran to Uhura and Kirk. He was pretty beat up, but he stood anyways. I slipped my hand underneath his arm to help him up. My knuckles started to burn.

"On behalf of Christopher Pike, my friend, I accept your surrender." he said. I paused, he actually killed Pike. A pang of guilt rose in my chest. He turned away and took a step forward before turning back to John, and bringing his fist to his face. Over and over again Jim hit him. John just smiled.

"Captain!" yelled Uhura. I looked over my shoulder at her. She stood there a look of worry on her face. I looked away from her to Spock. He looked like he was waiting to shoot the guy. Jim stopped out of breath. He looked up to meet Johns eyes.

"Captain?" John repeated. Jim turned his back to him and walked my way.

"Cuff him" he said to Spock. He looked at me

"are you alright?" he said worry spread in his voice.

"Yeah. I'm fine. What about you?" I said wiping some blood from the corner of his mouth. The movement surprised him, but he didn't move.

"Maybe a few broken ribs, but I'll be okay." he said smiling. I returned the smile. We all climbed back into the shuttle they came in on.

"Enterprise to Shuttle 1" Bones' voice came over the com on the shuttle.

"This is shuttle 1" Uhura answered.

"Is Captain Jones aboard?" he asked intensely.

"She's aboard Bones, and she's fine" she said. She looked to me and smiled. I smiled back and laid my head against the shuttle wall. I closed my eyes. It only took us 20 minutes to get to the Enterprise. When we arrived, Bones was there with a medical team. He ran up to me first.

"Are you alright?!" he said taking my face in his hands.

"I'm fine Bones, but Jim really needs your help right now" I said placing my hands over his and gently pulling them off my face. I gave him a kiss and walked past him to a remote part of the ship. It took me a minute to walk there, but I did. The observation deck was much smaller than the one on the Centerville. I sat on the bench that resided there and stared out to the vast nothingness of space. I was still in my grey officers uniform. It was now stained with dirt, sweat, and a small amount of blood from my knuckles. I didn't really care. Tears started down my face and onto my skirt. If there was anyone who resided on this ship that could destroy them all, it was John Harrison and his 72 torpedoes.


	3. Chapter 3

**A/N: Here's Ch. 3! I post as I get favorites/follows/reviews so do me a favor and please take 2 seconds out to do that! If you haven't already check out the first 2 installments of this story 'Forever United' and 'Changing Back Time' to get a better back drop! I also have a new Star Trek FF coming out soon called 'Madeline' so keep a look out for Ch. 1 of that one with in the next 2 weeks or so!**

**I sadly, own nothing except Captain Susan Jones, Commander Cassie Moore, and the U.S.S Centerville and her crew.**

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Ch. 3

*7 years ago*

"Ahh Lieutenant Jones, welcome. I want you to meet Commander John Harrison, you will be supervising him on a top secret weapon development ." said Admiral Marcus. I looked to the man in front of me. He was tall, slender yet strong, his piercing icy blue eyes radiated power, his dark black hair was slicked back and neat.

"Commander." I said nodding my head at the handsome man in front of me.

"Lieutenant" he returned his voice was deep and seductive. His eyes watched me with every step.

"I expect to have blueprints of what you are planning on my desk by 1300 hours on Monday. Understood?" said the admiral.

"Aye sir" we said in unison. I looked over to the Commander next to me. He returned the gaze, that's the moment I thought I fell in love with John Harrison.

*Present Day* I shot up straight in my bed. My shirt was damp with sweat. My hand was now wrapped up, but it burned as I used it to support my body from falling over. Bones told me that I was lucky I didn't need stitches. I placed my injured hand over Bones arm that lay limp in my lap. The dream of the moment I met Harrison burned in my mind. I looked over to him. His face still peaceful. I'm glad he was a heavy sleeper. I removed his hand from around my waist and left the room in my night clothes which consisted of a plain white shirt, and a pair of drawstring pants. I walked and walked thinking of nothing, but everything at the same time until I realized where my bare feet took me. The Brig. I stopped right before I could see him. My mind screaming at me to go back to sleep with Bones. That's when I heard voices.

"and what are you going to do? Punch me over and over again until your arm weakens, clearly you want to, so tell me, why am I still alive?" said John. Amusement in his voice.

"Everyone makes mistakes." said Jim. His cockiness getting in the way.

"Ahh. I know what it is. That girl. Susan yes. Did she ever tell you...about us?" he said. My heart stopped.

"What are you talking about?" said Jim clearly surprised.

"Ask her...about 7 years ago, and make sure you open up one of those torpedoes. Its the only way you will understand why I did what I did." said John. I heard Jim turn on his heal and walk my way. I didn't move. When he came around the corner he was stunned to see me.

"Suzie?" he said stopping. I grabbed his hand and pulled him into a closet at the end of the hallway. "What are you doing?" he said quietly.

"Do it. Ask me." I said waiting. He paused for a minute.

"Okay. What happened 7 years ago?" he asked crossing his arms across his chest.

"You never repeat this to Bones. Understood?" I said looking down to my feet.

"Yeah I got it." he said waiting for me to start talking. I took a deep breath. Me and Jim have gotten much closer since the whole thing with Cassie. He has always been someone she can talk to when she needed it, and he knew it. What he didn't know, is that she secretly loved him. She loved Bones also, a lot, but it always seemed as if the universe was pushing together Susan and Jim. I looked up to his electric blue eyes, that feeling filling my stomach. I couldn't take looking at him anymore, so I looked back down to my feet.

"When I was 19, I supervised the creation of class 1 weapons. My first assignment happened to be the creation of military grade torpedoes." I paused. I bit my lip to keep myself from weeping like a little girl. "The same ones aboard this ship." a tear started to fall down my cheek. "John Harrison designed the weapons. I happen to spend a lot of time with him." I said. The memories flooding my mind. I looked up to meet Jims eyes again this time the pieces clicking together like a giant jigsaw puzzle.

"So what are you saying...you and Harrison.." he said he put his hands on his hips and shook his head.

"I was young Jim. He was my first... everything." I said staring up to him. I wiped the tears from my eyes. "It was 7 years ago. I regret every waking moment." I said. My voice steady and harsh.

"Why does he want me to open a torpedo?" he asked rubbing his face with his hand.

"That...is nothing I can explain to you. You have to see it for yourself." I said pushing past him.

"Wait Suzie." said Jim as he grabbed my hand. "I don't care that you had a relationship with Harrison. But I need to know if you still love him." he said. I turned to face him quickly yanking my hand out of his. My knuckles began to bleed again from the movement, Bones will be angry with me, complaining that I needed to be more careful as he replaced the bandages. Anger spread throughout my body.

"Really Jim?" I said "I don't love that man! I never truly did. It was lust true lust. That was it. The only person in this world I dare to love is you!" I said. As soon as I said it. I knew I'd regret it. My hands flew to my mouth and my eyes widened. "I uh. I have to go. Bones is probably worried." I said turning and walking out of the closet without another word.


	4. Chapter 4

**A/N: Thanks to the new follower! I decided I need some feedback, so in order to get the next Ch. I need reviews! Tell me what I'm missing, if you like it, if you don't. Also I want to know if you want more Khan and Susan flashbacks? If so I can write some more in. Remember, this is the third installment! Check out the first 2 if you haven't already 'Forever United' and 'Changing Back Time'! Also have a new Star Trek FF called 'Madeline' coming out within the next 2 weeks so keep a look out for that. **

**I own nothing (sadly) except Captain Susan Jones, Commander Cassie Moore, and the U.S.S Centerville and her crew.**

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Ch. 4

When I got back to the room, Bones was gone. He left a note on my PADD saying he had to report to medical bay. I sighed. I reached to my nightstand and pulled out my com.

"Jones to Moore." I spoke. The line stayed dead. "Jones to Moore." i tried again. Nothing. I closed the small device and set it back down. I picked up my PADD and started to do some work. A few minutes later, My com went off.

"Kirk to Jones" it said. I picked it up.

"Jones here." I said standing up.

"Put on a uniform and report to the bridge. I need you." he said. I stood up and walked to my closet.

"Red or Gold?" I said a bit confused as to why both colors were there.

"Gold. You're a captain right?" he said.

"Yeah yeah. I'll be there in a sec. Jones out." I said closing the com. I really didn't want to see Jim after the events of earlier. I just had to put the memory in the back of my mind for now. I smoothed out the gold dress and yanked a brush through my tangled hair. I pulled it up into a high ponytail. I looked like myself. The gold captains pin shines against the gold of my uniform. I sat on the bed and yanked on my knee high regulation boots. I slipped my com into my boot, and picked up my PADD before walking out of the door. I figured I'd stop by Medbay before going to the bridge. It was on the way. When I got there, Bones was nowhere to be found. "He must be on the bridge" I thought to myself. I walked out and continued to the turbolift. I pressed the button for the Bridge and waited. When the door opened, people were gathered everywhere. "What's going on?" I said to Jim. He stood up and stood next to me. He tried desperately not to look me in the eyes, the tension clearly there. I continued to act normally. "Where's Bones?" I said looking around for him.

"He's on his way to that planet over there with Dr. Carol Marcus." he said giving up and looking over to me. I stared forward, ignoring his glance. I looked over to Uhura, a smirk forming on her face as she watched us clearly noticing the tension. She walked over to Sulu and held out her hand. He looked over to us sighing deeply and passed her a 20 dollar bill. I shook my head and let it go. I like Uhura so I didn't argue. I snapped back to our conversation.

"Carol Marcus? That's the Admirals daughter. He never lets her out into actual space. How did she get here?" I said stunned.

"She snuck aboard. Clever girl." he said clearly noticing the transaction between Uhura and Sulu. He smirked and looked forward. I shook my head not understanding something.

"She's a weapons specialist. Why-" I figured it out. I turned my whole body to face him. "Jim you sent Bones to help open a torpedo?! Why didn't you send me? I kind of have experience with these things!" I said trying to catch his eyes while crossing my arms over my chest.

"I figured you had enough excitement for the past few hours." he said shrugging his shoulders. He glanced over to me. I gave him a death glare. We stared for a second before a voice broke our concentration.

"McCoy to Enterprise." Bones' voice came over the intercom.

"Bones. How are things looking?" Said Jim looking away from me.

"You know, when I dreamed about being stuck on a deserted planet with a gorgeous woman, there was no torpedo." he said. I paused. Jealousy present on my face. Out of the corner of my eye I saw Uhuras mouth drop a bit.

"Bones you're not there to flirt." said Jim looking to me apologetically. I looked to him a bit angrily.

"Alright Doctor. What do we have here." said Bones clearly not paying attention to Jim.

"In order to open the missile, we have to get into the fuel compartment, after that we have access to the warhead." I heard. Her English accent very prominent.

"I once had to perform an emergency sea section of a gorgon before, Octuplets, and let me tell ya, those suckers bite. I think I can work some magic on your missile." he said. I was getting very irritated.

"Move." I told Jim. He took a step aside, gesturing me go go ahead. I placed my hands on the consul and leans forward. "Hey Bones. Maybe you can focus on the task at hand, and not the task in your pants." I said very irritated.

"Su?" he said surprised. I heard Carol in the background laugh a bit.

"Yeah." I said stepping away from the com and back to where I was standing. I looked back to Uhura, she looked to me and thumbed me up. I rolled my eyes and smiled a bit. Bones was pretty quiet until they started working.

"Alright Doctor. You're cutting the 26th wire down. Whatever you do, do not touch anything else." I heard Carol instruct. A few seconds later a weird noise happened, and Bones cried out.

"What happened?!" yelled Jim.

"My arms stuck!" yelled Bones clearly struggling to get it out. "It won't budge!"

"Sir the missile has armed itself" said Sulu. My heart started beating faster.

"Beam them up!" yelled Jim.

"Captain, the transporter cannot differentiate between Dr. McCoy and the torpedo, we cannot beam up one without the other." finished Spock. Jim looked to me. Panic quickly spread over my face. I was speechless

"Beam her up Jim!" yelled Bones over the com. I placed my hand on my stomach.

"You beam me up, he dies!" she yelled "Let me do this!" Kirk looked conflicted.

"We are locked on to Dr. Marcus' signal. Transporter ready on your command." said Sulu.

"10-9-8-7-6-5-4-3" I heard Chekov count. My body started to tremble with fear.

"Shit!" she yelled. There was a sound of wires breaking, and the countdown on the screen stopped.

"Bones are you alright?!" yelled Jim. There was no answer. More panic started to set In, my chest was heavy with grief. "Bones!" he yelled watching my face.

"Jim, you've gotta see this." Bones' voice said. I let out a breath I didn't even realize I was holding. Jim put his head down and smiled. I turned around and quickly walked off of the Bridge. I felt like I was going to throw up.

"Suzie wait!" I heard behind me. I stopped.

"What?" I said. Still breathless. I turned to face Jim.

"Are you alright?" he said examining me.

"My boyfriend was flirting with another woman, then almost dies. Im Not okay." I said putting my hands on my knees. I started to hyperventilate, tears started streaming down my face. I felt Jim stand me up.

"Calm down." he said embracing me into a hug. "He's on his way back Suzie." his warm embrace calmed me down. I layed my forehead against his chest. My small body fit into his body like a perfect fit to two puzzle pieces. I didn't want it to end.

"McCoy to Kirk." I heard coming from Jims pocket. He let me go and smiled.

"I have to get back to the bridge. Go get cleaned up and meet us in medbay." he said. I smiled and nodded.

"Aye captain." I said a bit playful. He turned around and started walking away.

"And remind your crew members to stop betting on who sleeps with who." I said before he rounded the corner. He stopped briefly and turned to face me he smiled and shook his head before resuming his steps. I turned around and headed back to my room. I washed my face with cold water and fixed my hair. My eyes were red and puffy from obvious crying. I dropped in some eye drops help get rid of the red, and dabbed on a bit of cover up to help with the red rims under my eyes. They were still puffy, but it wasn't as noticeable. I smoothed out my dress and made my way to medbay. When I walked into the room, everyone was there. I walked over to the torpedo and stood next to Jim. Bones looked up to me. I didn't look at him. He sighed and continued in with what he was saying.

"That's the weird thing about our friend here. He's 300 years old." everyone in the room paused. Jim scratched his head. I looked to the man in the cryotube. His face asleep. Everyone continued discussing. I backed up and slipped out of the room to walk to the brig. John Harrison stood up at my presence.

"Ahh. Susan. Looking lovely as ever." he said walking up to the glass wall.

"What are you trying to pull here Harrison?" I said crossing my arms over his chest. He smiled and looked down to his feet.

"Remember that night you found out I was hiding my crew in those weapons. You said you would help me, but you ran off to the the admiral and ratted me out." he said. His voice calm. The memory flooding back into my brain. "Well, I don't hate you Susan, you were being loyal to those who were loyal to you. I betrayed you. So you betrayed me. I simply want you to feel my pain as I take those you love away from you. Revenge on those who inflicted me pain." he said staring at me with those evil eyes. My mind flashed back as he talked.

*7 years ago*

John grasped my hand, he was gentle.

"You are so lovely" he said to me as he pulled me closer to him. His eyes were gleaming mischievously.

"And you are so charming." I said with a small laugh. He pulled his slender lips to mine. His kiss was tender, sweet. I closed my eyes and kissed him back. The passion was heavy. He picked me up and set me on the counter, my legs automatically wrapping around his small waist. He was slender, but strong. He pulled away.

"I love you my dearest Susan." he said looking deep into my soul with his cold eyes. "I'm not sure what I would do, if you were not mine" he said with the utmost sincerity.

I snapped out of my memory and smiled at him.

"Oh John. You do still love me. You simply want me for yourself." I said turning on my heel. Before I walked out I turned to look at him. Anger and surprise on his face. "You should really control your jealousy." I said as I stormed out of the brig. I walked back to my room. Bones stood there waiting for me.

"Hey Su, can we talk?" he said sitting down on the bed.

"You have 2 minutes." I said not paying much attention to him.

"I'm sorry I was flirting with someone else. You're just gettin' so distant from me since ya got on board." he said.

"So that gives you permission to flirt with another woman?" I said standing in front of him. He wrapped his arms around my waist and pulled me close. He turned his face up to meet my eyes. It was a bit weird to be taller than him.

"Of course not! I just thought you were getting to the point to where this wasn't working anymore. I thought you were ready to leave me. I didn't know what to do. I was stupid. I should have talked to ya" he said laying his forehead on my small stomach. I put my hand under his chin and turned his face to meet mine. I gave him a kiss. He smiled and pulled me down on the bed with him. I laughed as I landed on top of him. He kissed me passionately. We rolled around the bed of a few minutes, out lips never breaking. Pretty soon our clothes are on the floor next to us.


	5. Chapter 5

**A/N: Bo! Here's Ch.5, thank you for the review I recieved as well as the 2 additional followers! No one responded on the more Susan and Khan, so I went ahead and poster Ch. 5 without it. Remember please please please review! I update as I get favorites/follows/reviews. Also this is the third installment to this story, check out the first two if you haven't already, 'Forever United' and 'Changing Back Time'.**

**I own nothing (sadly) except Captain Susan Jones, Commander Cassie Moore, and the U.S.S her crew.**

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Ch. 5

I laid in bed with Bones for a few minutes. His arms around me.

"You know we have to get up." I said pushing myself up to lay my back against the headboard.

"I know. I just want to lay here for a few more minutes." he said. Laying his head in my lap. We laid there for about 10 more minutes before we felt a rattle shake the entire ship. We both looked at each other and jumped up to put our clothes back on.

"The Enterprise is in danger" I said picking up my com. I stood there and pulled on my boots. My hair fell in long curls down my back. I pulled it all up into a high ponytail. Like usual. Bones was nearly dressed. His blue shirt still laying on the bed. He picked it up and slid it over his head fast. We looked normal. "Lets get to the Bridge." I said running past him. He followed me out of the room and all the way to the Bridge. When we ran into the room, everything was quiet.

"Vulcans do not lie." said Spock. John was on the main screen. Holding Kirk hostage. My stomach dropped.

"Ahh. And there is one more negotiation." said John when he saw me run onto the Bridge. "Susan. I want her. Now." Bones snapped his head to me.

"No. I'm not giving her to ya." he said pulling me to him protectively. Spock turned to look at me. I looked to the Vulcan. We needed Jim back. I took a deep breath and stepped towards the large screen.

"Deal." I said. Bones ran up to me, but it was too late, the white circles encased my limbs. I turned to look at him. "I'll be back." I whispered to him. Then, I was on the Bridge of the U.S.S. Revenge. Kirk lay on the floor in front of John. Carol laid close to her deceased fathers body, she tried not to take glances over at him. She was holding her leg, it was obviously broken. Scotty layed close to Kirk. Passed out.

"Well Captain Kirk, it seems as if I should return you to your crew. A ship should never go down without her Captain." he said. I watched the buttons he typed on the screen, memorizing the equation he used. Kirk, Carol, and Scotty disappeared leaving me and John on the bridge alone.

"Why?" I asked buying time.

"I want you to witness, the death of the people you love." he said smiling.

"No John, I want the real reason you asked for me." I said crossing my arms over my chest.

"I have no idea what you are referring to Susan." he said not looking at me.

"I see it in your eyes John. Just tell me!" I yelled throwing my arms to my side. He ignored me

"Arm phasers." he said.

"Phasers armed." said the computer. He looked at me. His eyes burning into my soul. I panicked.

"Fire." he said. I looked out of the window to the small ship across from us. It was being hit heavily.

"John stop!" I yelled. He laughed. The firing stopped suddenly. He looked to the screen confused. A rumble shook through ship. I looked to the security monitors behind him. The lower decks were exploding.

"He armed the missiles." I said a smile crept up over my face. John looked to me. Sadness in his eyes to his newly lost crew.

"NO!" he yelled running out of the bridge. I used the opportunity I had at hand. I ran up to the screens and typed in the exact equation John did when he sent Kirk back to the Enterprise.

"Power low. Conformation needed."

"Confirmed!" I yelled. The white circles encased me once more. John walked back onto the bridge shell shocked.

"NO!" he yelled running toward me. It was too late. I appeared in medbay. Bones was strapping down patients.

"Wheres Jim!" I yelled to him. He looked up.

"Su!? I don't know!" he said obviously relieved to see her. I pulled my com out of my boot.

"Jones to Kirk!" I yelled. No answer. I closed it and ran out of medbay, Bones screaming after me. The ship started to shake. She was falling out of the sky. Gravitational bounds are going to fail soon. I ran onto the bridge.

"Spock!" I yelled. He looked up from the captains chair.

"Captain?" he said surprised.

"Yes yes I'm fine! Where's Jim?!" I yelled.

"I am not sure-" I didn't wait to hear what he had to say, instead, I turned and ran through the hallways. My feet started to slip, and before I knew it, I was falling. I looked below me there was Kirk. I reached next to me, my fingers grasped a railing. It pulled on my shoulder, but luckily I was light enough there wasn't much damage.

"Jim!" I yelled. He didn't hear me. "Jim!" I said louder. He looked up.

"Suzie!" he said the ship re positioned itself. We were able to stand.

"We need to get to engineering now!" I said.

"that's where we're going lad!" said Scotty running before us. We took off after him. The ship started to turn. We we're now running on the wall.

"Jump!" I hear Jim yell. I looked ahead. An opening to another hallway laid in front of us. I pushed with all my might. Jim and Scotty made it effortlessly. My leg slipped. I caught the edge before I fell. I hoisted myself up and continued running, ignoring the pain in my leg. I caught up to Jim and Scotty right as the ship decided to turn again. We laid flat against the railing when a large object hurtled its way toward us. I saw it first and held on as tight as I could. When it hit, Jim and Scotty were thrown over the side.

"I can't hold on!" yelled Scotty.

"Hold on!" warned Jim. Scotty slipped and my heart dropped for a slight moment before Jim caught his hand. Jim wasn't going to be able to hold on much longer. I reached as far as I could to Jims hand, but I slipped. My legs fell through. I looked up to see Chekov making his way towards us. He was fast. Just as Jim slipped from the bars, Chekov threw himself at the captain. He got him. Jim looked up surprised.

"Chekov!" he smiled

"I got you Keptin!" yelled Chekov struggling. I swung my legs back up and steadied myself. The ship returned to its Normal position. I helped Chekov pull Scotty and Jim up. We were all standing there hands on our knees, catching our breath.

"We have to redirect the power. If we don't all of this will be useless." I said breathless. Scotty looked at me.

"Aye, she's right captain. There's a switch. It-" I cut him off.

"I know where its at, Chekov come with me." I said grabbing the young ensigns arm, running to the set of stairs right before the warp core. I looked back and saw Jim run with Scotty to the engineering console. Me and Chekov ran through corridors. The ship turned again and we slipped down a hallway. I grabbed Chekovs hand, and clutched onto a pole with my free hand.

"Don't worry Chekov! I got you!" I yelled down to the boy. He looked up. Terror on his face to what lay bellow if I didn't catch him. When The ship leveled out, we stood up and continued running. We finally reached it. Chekov removed the lid and flipped the switch. "Strap in!" I yelled to him.

"Aye Keptin!" he yelled sitting in the empty seat next to me. The straps securing us in place. The next 3 minutes were hell. I looked to Chekov, he was scared. I grabbed his hand in reassurance. He looked to me grateful. His face, could be the last I ever see. I thought of Bones and Jim. My heart started to break. Suddenly the lights came on and the ship steadied herself. Chekov let out a large breath.

"Ve saved her!" he yelled through his thick accent. I paused. The redirection of power should have taken place almost immediately after we flipped the switch.

"Something's wrong." I said to him, he looked at me puzzled. I removed the straps and ran to the engineering deck. Chekov followed. My com went off. I stopped momentarily and pulled it out of my boot.

"Scotty what is it?!" I said panicked.

"Just get down here" he said I closed my com and continued running. When I got there, Spock was at the entrance of the warp core, Uhura was standing by Scotty, her hand over her mouth. I put my hands behind my head as Scotty turned around to face me and Chekov. Tears in his eyes.

"No." I said. My eyes started to burn. Scotty looked down. "No." I said my voice cracking I looked into the door. Chekov pulled me into a hug. I couldn't help but look past his shoulder, to Jim...dead. I felt my knees weaken and I dropped looking into his lifeless eyes. Chekov caught me and gently set me on the ground while kneeling next to me. I didn't hear Spock yell and run out of engineering. I didn't see Scotty walk over to me. I didn't feel Uhuras hands on my back. The only thing I saw was Jims lifeless eyes, the only thing I felt was my heart being ripped out of my chest, and the only thing I heard was Jims voice in my head. "I love her Bones."

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**A/N: It killed me writing this Ch. Let me know how Susans reaction to Kirks death made you feel! A lot more heart break next Ch.! But something that has to be done! -CommanderJames**


	6. Chapter 6

**A/N: Okay so here's Ch.6. Thank you for the review I got! I'm glad you're enjoying it! Only 1 Ch. Left after this! Sorry this Ch.s a bit shorter than the rest, but it accomplishes what it needs to. Remember this is the third installment of my Susan Jones trilogy, if you haven't read the first 2, you may not get some of the things that happen in this Ch. So check those both out.**

** I own nothing (sadly) except Captain Susan Jones, Commander Cassie Moore, and the U.S.S. Centerville and her crew.**

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Ch.6

I wouldn't get up. Even when they came to take Jims body away. I just sat there in front of the door where Jim died with my legs crossed, staring. I stopped crying. I stopped talking. What if this is my fault? Because I cheated death. This all happened because I was still alive. Jims days started to count down the moment my destiny changed. I lifted my hand to the clear fingerprints on the other side of the chamber where the last place Jims hand rested when he was slowly dying. My body started to shake with anger. Hot tears poured down my face. I couldn't do this. I lost him. I loved him. I hid behind a man I loved so little in comparison to the man I truly loved because of fear. Because I feared death more than I wanted happiness. If I could have Jim back for just one moment, I would tell him everything. Bones was sweet, and yes I loved him, but he wasn't my other half. He wasn't my soul mate. He was a shadow to shield me from my real feelings. I closed my eyes and remembered everything Jim once told me, I remembered Jims face, I remembered...I felt the world around me start to spin. I opened my eyes to a whole other setting. Jim stood in front of a casket. His eyes red rimmed. I stood up from the from the grassy area behind the casket, and walked around next to him. I looked down. The person was me. It didn't phase me. I've seen this a million times. I looked over to see Bones standing behind a podium. He could barely speak.

"I loved Su for 4 years. Her bravery, her heart, her-" he stopped for a minute and gripped the sides of the podium. "Her sacrifice to save a ship that wasn't even hers." I stopped moving and listened. "She bravely climbed into the warp core, realigned it, and died a hero." he said taking a shaky breath. That's how Jim died. I looked around to the devastated people. Uhura, Moore, Chekov, Davenport. My eyes wandered over them over and over until I spotted something in the back. Myself. I walk towards her. She's staring at me. I paused. She can see me? I thought as I resumed my steps. When I get within ear range she says:

"Beautiful isn't it?"

"What? Our own funeral?" I said standing next to my identical twin. She smiles. "The way these people cared for us." She said looking at me. She paused and studied me for a minute. "Wait. You're still alive." she said astonished. "Your destiny has changed." she said switching her eyes back to the ceremony. "you changed it. Defied it. You're the living." I closed my eyes.

"At the cost of Jims life." I said quietly while looking down at my hands. Tears pricked the back of my eyes. One escaped and fell down my cheek.

"Oh no. Jim always lives a full life." she said a bit amused with my sadness.

"what do you mean?" I said turning my entire body to face her. Her hair was messed up, her dress ripped. She Was shaking slightly. Her eyes weren't the same shade of hazel, they had a grey tint to them. Her chocolate brown skin was very pale, sickly looking. A sudden realization came over me. I felt a bit sick. "This is your funeral." I said. She turned to me.

"Yeah. Sadly not all of us are you, happy healthy. Most of our lives are a tragedy, filled with nothing but pain and punishment. We did nothing to deserve it, life just happens to be cruel." she said. A small tear rolling down her face as Cassie started up to the microphone.

"I'm really sorry." I said I looking down to my feet. "I need to know what you ment by Jim lives a full life" I said crossing my arms over my chest and looking back up to meet her dead eyes.

"Just go back to your own reality. You'll see." she said. At that moment I was back. My hand still rested on the window. I stood up and ran towards medbay. Bones sat at his desk his head in his hands.

"Get a cryotube!" I yelled to him he looked up astonished.

"what?!" he said. Tears on his face.

"Its going to come along I know it! Get that man into an induced coma, put Jims body into the tube now!" I screamed at the nurse. She looked to Bones. He shrugged.

"Aye Captain." she said grabbing a team and following orders.

"What's the plan?" asked Bones standing from his chair.

"I'm not sure yet." I said looking around. I heard a faint beeping sound in the corner of the room. I turned my head and there was my answer. "Johns blood." I said staring at the tribble that just started to breathe. Why didn't i think of it before?!Bones turned around. When he spotted the tribble, he smiled. He took off towards a console in the middle of medbay.

"McCoy to Spock!" he tried. Nothing. "McCoy to Bridge!" he tried.

"Sulu here!" he yelled.

"I need you to get a hold of Spock! We need John alive! I think he can save Jim!" he said walking over to the cryotube. He pressed a few buttons and Jims body froze. He looked to me. "How did you know?" he said puzzled.

"Lets just say. I saw the light." I said walking past Bones to Jims body. I heard Bones take a deep breath.

"Su. We need to talk." he said softly, obviously observing my actions. I took a deep breath and crossed my arms over my chest.

"Yeah I think we do." I said turning to face him. A few tears streamed down his face, not from the death of Jim, but for what was coming up next.

"I uhh knew for a while." he said smiling. It was a sad smile. "Knew that you would eventually choose him" he said fiddling with a tool he held in his hand. I looked down to my feet and listened. "I never proposed because of that reason. The doubt in my mind that you were actually going to stay with me was really strong." he said taking a shaky breath. "I promised myself, that when you did choose him, that I would let chya go." he looked up to the ceiling and placed his hands on his hips. He looked back down to me as I lifted up my head. I made the mistake of meeting his eyes, his sad sad eyes. Tears started down my face faster. "This is me Su...lettin' ya go." he said. He let a few tears leave his eyes before wiping them away. A relationship that impacted us both was now over. I pulled him into a hug. He held me tightly, As I did with him. Part of me didn't want me to end, but I knew it had to. I let him go.

"I do love you Bones. I really do." I said turning my back and walking out of medbay my hand over my mouth, I felt like I was going to puke. I never thought leaving him would be so hard.

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**A/N: Sorry to those who were hoping for a happy ending with Susan and Bones! I hated this Ch. So much! So much heartbreak! Now Suzie can be with the one she loves c: review guys please! I'll be uploading Ch. 7 tomorrow regardless if I get followers/favorites/reviews, but reviews would be great C: next Ch. Balances out this I've so stay tuned c: -CommanderJames**


	7. Chapter 7

Ch. 7

Jim has been in a coma for 2 weeks. I sat next to him. He had a steady heart rate. The transfusion went according to plan. His cells no longer heavily radiated. He was alive...and so was I. Bones came in every hour to check his vitals. Things were kinda awkward at first, but things fell back into place soon after he started to date Carol Marcus. She made him happy. We talked when he had the chance. Had lunch with me all the time. The thing I really had to get used to was the sleeping alone. When I got back, I started to sleep in Cassies room again. She didn't mind. She was relieved when I came knocking on her door. Her hair was messed up, and her eyeliner smeared down her face like she had been crying for days, she embraced me into a hug and told me about her horrors of the past few days, how she nearly broke down when she found out I was missing. We talked for hours. Told her about everything, Bones, the visions I've had, John, and Jim. She listened and understood. I shook my head clear of the memories that flooded my head when I heard Jim start to move.

"Suzie?" he said looking to me. I stood up from my chair and ran to his side.

"Jim!" I said grabbing his hand. "Bones!" I yelled. He came rushing in. Jim was confused as to how he was alive, so I explained how Bones, Uhura, and Spock saved his life. I looked to the door and in came Spock. Carol right behind him dressed up.

"Bones, Carols here." I said turning to him. Bones hesitated a bit, but when I nodded my head to him, said his goodbyes and walked out to his newly found girlfriend.

"Wait. I thought-" he said obviously confused. I smiled at him.

"We broke up." I said looking him in the eye.

"Why?" he said putting the pieces together in his head. I didn't answer him, instead I just stretched over the bed and gave him a long passionate kiss. A kiss I longed for. Spock cleared his throat. We broke apart

"Maybe I should come back whe-" he said. I intervened.

"No no. I'll wait outside" I said smiling down to Jim. I walked outside of the room and got some water from the cafeteria downstairs. I waited about 10 minutes before returning. I walked back into the room when I was positive that Spock was gone. When Jim spotted me, his eyes lit up.

"so about that kiss." he said sitting up.

"You and Bones broke up because of me?" he said worried.

"No of course not. We just felt it was time. I was in love with someone else, he knew we were going to end. So we broke it off before anymore damage could be done" I said grabbing his hand. He smiled to me.

"Kiss me again." he said. I lowered my lips to his. "and by the way. I'm in love with you too." he said eyes closed in anticipation. I smiled and kissed him, this kiss marked the end of one chapter in our lives, and the beginning of another with each other...finally.

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A/N: Well guys it pains me to tell you...its over. I may write a 4th one, but it won't be for a while. Remember if you're gonna miss Susan, she qill be featured in my new FF 'Madeline' that is currently in the works. For my followers I will put a preview up soon! Or just the first Ch. I think 'Madeline' will be my best FF so look out for that! I thank you guys for sticking with me through these 3 stories! Let me know if you want more Susan and Kirk FFs and I can probably pull together some one shots! We shall see


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